Growing season drives the compositional changes and assembly processes of epiphytic bacterial communities of two submerged macrophytes in Taihu Lake

2020 ◽  
Vol 96 (4) ◽  
Author(s):  
Dan He ◽  
Lijuan Ren ◽  
Qinglong L Wu
Keyword(s):  
Stochastic Processes ◽  
Bacterial Communities ◽  
Taihu Lake ◽  
Submerged Macrophytes ◽  
Geographic Distance ◽  
Null Model ◽  
Alpha Diversity ◽  
Growing Season ◽  
Epiphytic Bacteria ◽  
Alpha And Beta Diversity

ABSTRACT Large amounts of epiphytic bacteria live on the leaf surfaces of submerged macrophytes in freshwater lakes. Despite their important roles in affecting host plant's health and biogeochemical cycling, knowledge about epiphytic bacteria assembly is not sufficient. We studied epiphytic bacteria on two cohabiting plant species in Taihu Lake, China. In comparison with plant identity and geographic distance, the plant-growing season played a prominent role in driving alpha and beta diversity (compositional variations) of epiphytic bacterial communities. Phylogeny-based null model analysis revealed that the growing season also drove the relative importance of deterministic versus stochastic processes underlying bacterial community assembly. In May when both plants start growth, the deterministic processes were most prominent, while in months later than June, the stochastic processes’ effects increased substantially. In addition, we found a significant positive relationship between alpha diversity and compositional stochasticity, implying that stochastic processes may have great effects on the maintenance of diversity and functioning of epiphytic bacteria in aquatic ecosystems. In summary, the growing season overwhelmed plant identity and spatial site in shaping epiphytic bacterial communities in Taihu Lake, which may suggest new clues in understanding the dynamics of epiphytic communities and their roles in large shallow lacustrine ecosystems.

scholarly journals Gut microbiota composition is associated with narcolepsy type 1

2020 ◽  
Vol 7 (6) ◽  
pp. e896
Author(s):  
Alexandre Lecomte ◽  
Lucie Barateau ◽  
Pedro Pereira ◽  
Lars Paulin ◽  
Petri Auvinen ◽  
...  
Keyword(s):  
Community Structure ◽  
Gut Microbiota ◽  
Bacterial Communities ◽  
Beta Diversity ◽  
Alpha Diversity ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Differential Abundance ◽  
Alpha And Beta Diversity

ObjectiveTo test the hypothesis that narcolepsy type 1 (NT1) is related to the gut microbiota, we compared the microbiota bacterial communities of patients with NT1 and control subjects.MethodsThirty-five patients with NT1 (51.43% women, mean age 38.29 ± 19.98 years) and 41 controls (57.14% women, mean age 36.14 ± 12.68 years) were included. Stool samples were collected, and the fecal microbiota bacterial communities were compared between patients and controls using the well-standardized 16S rRNA gene amplicon sequencing approach. We studied alpha and beta diversity and differential abundance analysis between patients and controls, and between subgroups of patients with NT1.ResultsWe found no between-group differences for alpha diversity, but we discovered in NT1 a link with NT1 disease duration. We highlighted differences in the global bacterial community structure as assessed by beta diversity metrics even after adjustments for potential confounders as body mass index (BMI), often increased in NT1. Our results revealed differential abundance of several operational taxonomic units within Bacteroidetes, Bacteroides, and Flavonifractor between patients and controls, but not after adjusting for BMI.ConclusionWe provide evidence of gut microbial community structure alterations in NT1. However, further larger and longitudinal multiomics studies are required to replicate and elucidate the relationship between the gut microbiota, immunity dysregulation and NT1.

Stochastic processes dominate marine free-living Vibrio community assembly in a subtropical gulf

2020 ◽  
Vol 96 (11) ◽  
Author(s):  
Nan Li ◽  
Ke Dong ◽  
Gonglingxia Jiang ◽  
Jinli Tang ◽  
Qiangsheng Xu ◽  
...  
Keyword(s):  
Stochastic Processes ◽  
Trophic State ◽  
Heterotrophic Bacteria ◽  
Variation Partitioning ◽  
Geographic Distance ◽  
Alpha Diversity ◽  
Mantel Test ◽  
Beibu Gulf ◽  
Assembly Features ◽  
Marine Environmental

ABSTRACT Understanding the effects of eutrophication on heterotrophic bacteria, a primary responder to eutrophication, is critical for predicting the responses of ecosystems to marine environmental pollution. Vibrio are indigenous in coastal water and of significance to geochemical cycling and public health. In this study, we investigated the diversity and assembly features of Vibrio, as well as their relationship with the environmental factors in the subtropical Beibu Gulf. We found that the alpha diversity of Vibrio increased in parallel with the trophic state they occupy. A Mantel test indicated that the trophic state was correlated to Vibrio beta diversity and the correlation gradually strengthened at higher trophic states. Variation partitioning analysis suggested that the geographic distance was an important factor impacting the variables of Vibrio communities in all the samples, but nutrients exerted more influence in the more highly eutrophic samples. Our results demonstrated that stochastic processes govern the turnover of marine Vibrio communities in the Beibu Gulf and that ecological drift was the most important process for assembly of the Vibrio communities.

scholarly journals Dynamic and Assembly of Benthic Bacterial Community in an Industrial-Scale In-Pond Raceway Recirculating Culture System

2021 ◽  
Vol 12 ◽  
Author(s):  
Yiran Hou ◽  
Bing Li ◽  
Gangchun Xu ◽  
Da Li ◽  
Chengfeng Zhang ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Stochastic Processes ◽  
Microbial Communities ◽  
Bacterial Communities ◽  
Culture System ◽  
Null Model ◽  
Dispersal Limitation ◽  
Industrial Scale ◽  
Ecological Processes ◽  
Benthic Microbial Communities

To reduce water utilization, limit environmental pollution, and guarantee aquatic production and quality, the in-pond raceway recirculating culture system (IPRS) has been developed and is widely used. The effectiveness and sustainability of IPRSs rely on a good understanding of the ecological processes related to bacterial communities in the purification area. In this study, we investigated the dynamics and assembly mechanisms of benthic bacterial communities in the purification area of an industrial-scale IRPS. We found significant temporal and spatial variations in the sediment characteristics and benthic bacterial communities of the IPRS, although correlation analyses revealed a very limited relationship between them. Among the different culture stages, we identified numerous benthic bacteria with different abundances. Abundances of the phyla Bacteroidota and Desulfobacterota decreased whereas those of Myxococcota and Gemmatimonadota increased as the culture cycle progressed. Co-occurrence networks revealed that the bacterial community was less complex but more stable in the IPRS at the final stage compared with the initial stage. The neutral community model (NCM) showed that stochastic processes were the dominant ecological processes shaping the assembly of the benthic bacterial community. The null model suggested that homogenizing dispersal was more powerful than dispersal limitation and drift in regulating the assembly of the community. These findings indicate that the benthic microbial communities in purification areas of the IPRS may not be affected by the deposited wastes, and a more stable benthic microbial communities were formed and mainly driven by stochastic processes. However, the benthic microbial communities in the purification area at the end of the culturing stage was characterized by potentially inhibited organic matter degradation and carbon and sulfur cycling abilities, which was not corresponding to the purification area’s function. From this point on, the IPRS, especially the purification area was needed to be further optimized and improved.

scholarly journals Fungal and bacterial communities of ‘Pinot noir’ must: effects of vintage, growing region, climate, and basic must chemistry

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e10836
Author(s):  
Kerri L. Steenwerth ◽  
Ian Morelan ◽  
Ruby Stahel ◽  
Rosa Figueroa-Balderas ◽  
Dario Cantu ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
Geographic Distance ◽  
Growing Season ◽  
Pinot Noir ◽  
Growing Degree Days ◽  
Degree Days ◽  
The Family ◽  
Growing Region ◽  
Growing Season Precipitation ◽  
Grape Musts

Background The geographic and temporal distributions of bacterial and fungal populations are poorly understood within the same wine grape cultivar. In this work, we describe the microbial composition from ‘Pinot noir’ must with respect to vintage, growing region, climate, and must chemistry across the states of California and Oregon, USA. Materials and Methods We sampled ‘Pinot noir’ clone 667 clusters from 15 vineyards existing in a latitudinal gradient spanning nearly 1,200 km in California and Oregon for two vintages (2016 and 2017). Regions included five American Viticultural Areas (AVA). In order from southern California to Oregon, these AVAs were Santa Barbara, Monterey, Sonoma, Mendocino, and Willamette Valley. Uninoculated grape musts were subjected to 16S rRNA gene and ITS-1 amplicon sequencing to assess composition of microbial communities. We also measured grape maturity metrics. Finally, to describe regions by precipitation and growing degree days, we queried the Parameter-elevation Regressions on Independent Slopes Model (PRISM) spatial climate dataset. Results Most of the dominant bacterial taxa in must samples were in the family Enterobacteriaceae, notably the lactic acid bacteria or the acetic acid bacteria groups, but some, like the betaproteobacterial genus Massilia, belonged to groups not commonly found in grape musts. Fungal communities were dominated by Hanseniaspora uvarum (Saccharomycetaceae). We detected relationships between covariates (e.g., vintage, precipitation during the growing season, pH, titratable acidity, and total soluble solids) and bacterial genera Gluconobacter and Tatumella in the family Enterobacteraceae, Sphingomonas (Sphingomonodaceae), Lactobacillus (Lactobacillaceae), and Massilia (Oxalobacteraceae), as well as fungal genera in Hanseniaspora, Kazachstania, Lachancea, Torulaspora in the family Saccharomycetaceae, as well as Alternaria (Pleosporaceae), Erysiphe (Erysiphaceae), and Udeniomyces (Cystofilobasidiaceae). Fungal community distances were significantly correlated with geographic distances, but this was not observed for bacterial communities. Climate varied across regions and vintages, with growing season precipitation ranging from 11 mm to 285 mm and growing degree days ranging from 1,245 to 1,846. Discussion We determined that (1) bacterial beta diversity is structured by growing season precipitation, (2) fungal beta diversity reflects growing season precipitation and growing degree days, and (3) microbial differential abundances of specific genera vary with vintage, growing season precipitation, and fruit maturity metrics. Further, the correlation between fungal community dissimilarities and geographic distance suggests dispersal limitation and the vineyard as a source for abundant fungal taxa. Contrasting this observation, the lack of correlation between bacterial community dissimilarity and geographic distance suggests that environmental filtering is shaping these communities.

scholarly journals Temporal Variation in the Ecological Functioning of Benthic Communities After 20 Years in the Eastern Mediterranean

2021 ◽  
Vol 8 ◽  
Author(s):  
Irini Tsikopoulou ◽  
Panagiotis D. Dimitriou ◽  
Ioannis Karakassis ◽  
Nikolaos Lampadariou ◽  
Nadia Papadopoulou ◽  
...  
Keyword(s):  
Stochastic Processes ◽  
Eastern Mediterranean ◽  
Species Abundance ◽  
Null Model ◽  
Large Data ◽  
Aegean Sea ◽  
Functional Composition ◽  
Data Set ◽  
Alpha And Beta Diversity ◽  
Functional Richness

Marine benthic ecosystems face well-documented changes as a result of human activities. Describing these changes is important for predicting ecosystem functioning. In this context, long-term changes in soft-bottom macrofaunal communities after a quarter of a century were studied in the south Aegean Sea with the purpose of investigating whether temporal changes in taxa diversity are accompanied by changes in functional diversity, and secondly to determine the main mechanisms driving these changes (i.e., deterministic versus stochastic processes). To achieve this, a large data set that included species abundance data collected in 1990 and 2014 from several sampling sites along a transect line was used. A biological trait analysis (BTA) was conducted to determine the species functional roles. The results revealed a decline in taxonomic alpha and beta diversity metrics between 1990 and 2014, a difference that was also reflected in functional richness, partially in functional redundancy, but not in functional composition. The stability of functional composition indicated that replacements of functionally similar taxa may occur, ensuring the resilience of the ecosystem to provide goods and services. Finally, the comparison of co-occurrence and functional networks for 1990 indicated a non-differentiation with the null model and, it was not possible to determine if the benthic community was structured due to stochastic processes (e.g., dispersal, natural phenomena) or an overlap of deterministic processes (e.g., niche-filtering, competition). In contrast, the comparison of networks for 2014 pointed out that environmental conditions have acted as a major filter on species distribution.

Alpha- and beta- diversity of woody species across environmental gradients in African and Australian tropical savannas

2020 ◽  
Author(s):  
Felix Trotter ◽  
Caroline Lehmann ◽  
Keyword(s):  
Beta Diversity ◽  
Woody Plant ◽  
Environmental Gradients ◽  
Species Turnover ◽  
Geographic Distance ◽  
Alpha Diversity ◽  
Woody Species ◽  
Mean Annual Temperature ◽  
Alpha And Beta Diversity ◽  
Rainfall Seasonality

<p>Patterns of woody plant diversity in the tropical savanna biome has received little research attention but is relevant to understanding the complex vegetation dynamics of a biome that have remained contentious for almost a century. Tropical savannas of Africa and Australia are defined by the co-existence of woody plants and grasses, and the evolution and assembly of the savanna biome trace back 3-10 million years. Here, we explored patterns of local (alpha-) diversity and species turnover (beta-diversity) of woody plant species across African and Australian savannas. We aimed test the relative role of the environmental gradients of rainfall, temperature, fire and soil in shaping the relative abundance of all of woody species, genera, and families. Using generalized additive models (GAMs) and generalised dissimilarity models (GDMs) of field inventory data from vegetation plots across sub-Saharan Africa and Northern Australia we analysed changes in alpha- and beta-diversity. Environmental gradients were characterised as effective rainfall (ER), rainfall seasonality (coefficient of variation of monthly rainfall), mean annual temperature (MAT), temperature seasonality, fire frequency, and cation exchange capacity (CEC) in soils.</p><p>Savannas in Australia are on average drier and hotter than in Africa likely as a product of lower altitude. Crucially, diversity across all taxonomic levels is approximately two to three times greater in Africa compared with Australia. Within each continent, rainfall seasonality was the strongest environmental correlate of both alpha- and beta-diversity. In Africa, there is a strongly negative relationship between alpha-diversity at all taxonomic levels and rainfall seasonality. In contrast, in Australia, the relationship between alpha-diversity and rainfall seasonality while relevant is non-linear. Surprisingly within continents, rainfall, temperature, soils and fire had little bearing in these data on patterns of alpha diversity.</p><p>In terms of beta-diversity, and likely linked to the overall differences in diversity between continents, the geographic distance equalling total species turnover is greater in Australia than in Africa. Effective rainfall was the only additional significant correlate of woody species turnover in Australia, but only in arid regions. In Australia, at higher taxonomic levels the capacity of GDMs to explain variation in the data diminished substantially as a product of low diversity in genera and families. When compared to Australia, species turnover in Africa increases when geographic distance, rainfall seasonality and mean annual temperature are relatively low.</p><p>Our findings highlight that with ongoing climate change specifically with shifts in rainfall distribution that will also affect local drought regimes, rainfall seasonality could substantially alter patterns of diversity, specifically in Africa. There have been persistent attempts to explain ecosystem dynamics in savannas with respect to climate, soils and fire with emphasis often on total rainfall, but our findings suggest that rainfall seasonality can have strong effects on diversity that may interact with other environmental correlates such as fire.</p>

scholarly journals The Composition and Assembly of Bacterial Communities across the Rhizosphere and Phyllosphere Compartments of Phragmites Australis

Diversity ◽  
2019 ◽  
Vol 11 (6) ◽  
pp. 98 ◽  
Author(s):  
Qi Zhou ◽  
Xiaomin Zhang ◽  
Rujia He ◽  
Shuren Wang ◽  
Congcong Jiao ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Phragmites Australis ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Null Model ◽  
Rrna Gene ◽  
Rare Taxa ◽  
Alpha And Beta Diversity ◽  
Deterministic Processes ◽  
The Difference

The rhizosphere and the phyllosphere represent two different epiphytic compartments of host plant, which are closely related to plant growth, health, and productivity. However, the understanding of the diversity, composition, and assembly of the bacterial communities in different epiphytic microenvironments of large emerged macrophytes has remained elusive, especially the abundant and rare taxa across rhizosphere and phyllosphere communities. In this study, we collected samples of two different epiphytic compartments (rhizosphere and phyllosphere) of Phragmites australis. Both 16S rRNA gene-based high-throughput sequencing and null-model analysis were employed to determine the difference in the composition and assembly of above-mentioned epiphytic bacterial communities. Our results indicated that bacterial communities of rhizosphere exhibited higher diversity and richness than those of phyllosphere. Deterministic processes dominated the assembly of bacterial community in both compartments, and stochastic processes contributed a certain proportion (30.30%) in the assembly of phyllosphere bacterial community. We also found that rare taxa contributed more significantly to the alpha- and beta-diversity of bacterial community than those of abundant taxa. The obtained data are useful for better understanding the bacterial community of different epiphytic compartments of P. australis.

scholarly journals Geographical Distribution of Iron Redox Cycling Bacterial Community in Peatlands: Distinct Assemble Mechanism Across Environmental Gradient

2021 ◽  
Vol 12 ◽  
Author(s):  
Liang Yang ◽  
Ming Jiang ◽  
Yuanchun Zou ◽  
Lei Qin ◽  
Yingyi Chen
Keyword(s):  
Bacterial Community ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Geographic Distance ◽  
Null Model ◽  
Redox Cycling ◽  
Biogeographic Patterns ◽  
Deterministic Processes ◽  
Iron Redox ◽  
Soil And Water

Microbial-mediated iron (Fe) oxidation and reduction greatly contribute to the biogeochemistry and mineralogy of ecosystems. However, knowledge regarding the composition and distribution patterns of iron redox cycling bacteria in peatlands remains limited. Here, using high-throughput sequencing, we compared biogeographic patterns and assemblies of the iron redox cycling bacterial community between soil and water samples obtained from different types of peatland across four regions in Northeast China. A total of 48 phylotypes were identified as potential iron redox bacteria, which had greater than 97% similarity with Fe(II)-oxidizing bacteria (FeOB) and Fe(III)-reducing bacteria (FeRB). Among them, Rhodoferax, Clostridium, Geothrix, Sideroxydans, Geobacter, Desulfovibrio, and Leptothrix could be used as bioindicators in peatlands for characterizing different hydrological conditions and nutrient demands. Across all samples, bacterial communities associated with iron redox cycling were mainly affected by pH, dissolved organic carbon (DOC), and Fe2+. Distance–decay relationship (DDR) analysis indicated that iron redox cycling bacterial communities in soil, but not in water, were highly correlated with geographic distance. Additionally, null model analysis revealed that stochastic processes substituted deterministic processes from minerotrophic fens to ombrotrophic bogs in soils, whereas deterministic processes were dominant in water. Overall, these observations suggest that bacteria involved in iron redox cycling are widespread in diverse habitats and exhibit distinct patterns of distribution and community assembly mechanisms between soil and water in peatlands.

scholarly journals Study on the diversity of epiphytic bacteria on corn and alfalfa using Illumina MiSeq/NovaSeq high-throughput sequencing system

2021 ◽  
Vol 71 (1) ◽  
Author(s):  
Meixiao Wu ◽  
Yuehua Wang ◽  
Yijing Wang ◽  
Xuefei Wang ◽  
Ming Yu ◽  
...  
Keyword(s):  
High Throughput ◽  
Beta Diversity ◽  
High Throughput Sequencing ◽  
Raw Materials ◽  
Alpha Diversity ◽  
Illumina Miseq ◽  
Diversity Indices ◽  
Epiphytic Bacteria ◽  
Alpha And Beta Diversity ◽  
Paired End Sequencing

Abstract Purpose To investigate the diversity of the epiphytic bacteria on corn (Zea mays) and alfalfa (Medicago sativa) collected in Hengshui City and Xingtai City, Hebei Province, China, and explore crops suitable for natural silage. Methods The Illumina MiSeq/NovaSeq high-throughput sequencing system was used to conduct paired-end sequencing of the community DNA fragments from the surface of corn and alfalfa collected in Hengshui and Xingtai. QIIME2 and R software were used to sort and calculate the number of sequences and taxonomic units for each sample. Thereafter, the alpha and beta diversity indices at of species level were calculated, and the abundance and distribution of taxa were analyzed and compared between samples. Result At phylum level, the dominant groups were Proteobacteria (70%), Firmicutes (13%), Actinobacteria (9%), and Bacteroidetes (7%). Meanwhile, the dominant genera were Pseudomonas (8%), Acinetobacter (4%), Chryseobacterium (3%), and Hymenobacter (1%). Enterobacteriaceae (24%) were the most predominant bacteria in both the corn and alfalfa samples. Alpha diversity analysis and beta diversity indices revealed that the diversity of epiphytic microbial communities was significantly affected by plant species but not by region. The diversity and richness of the epiphytic bacterial community of alfalfa were significantly higher than those of corn. Conclusion This study contributes to the expanding knowledge on the diversity of epiphytic bacteria in corn and alfalfa silage and provides a basis for the selection of raw materials.

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